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feat: bwa-meme picard option #558
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christopher-schroeder
changed the title
typo in rule naming, reactivate picard option, picard test
feat: bwa-meme picard option
Sep 20, 2022
johanneskoester
approved these changes
Oct 10, 2022
Phlya
pushed a commit
to Phlya/snakemake-wrappers
that referenced
this pull request
Jan 10, 2023
* typo in rule naming, reactivate picard option, picard test * wrongly configured test * wrongly configured test again * genome wildcard is now hardcoded in test * wrapper path * dont use other wrappers in test * dont use other wrappers in test * environment.yaml in test * try again wrapper in test * try index wrapper again * use all rule * version index wrapper * remove index env * used_wrappers.yaml * used_wrappers.yaml * swap for github action * swap 10g * swap 20g * number of model parameters in index to decrease resource consumption for test * revert swap size * different approach, zipped file now * snakefmt, black * log for extraction * conda for gzip to satisfy linter * add the yaml * mbuffer to 2g
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Description
QC
For all wrappers added by this PR,
input:
andoutput:
file paths in the resulting rule can be changed arbitrarily,threads: x
statement withx
being a reasonable default,map_reads
for a step that maps reads),environment.yaml
specifications follow the respective best practices,input:
oroutput:
),Snakefile
s and their entries are explained via comments (input:
/output:
/params:
etc.),stderr
and/orstdout
are logged correctly (log:
), depending on the wrapped tool,tempfile.gettempdir()
points to (see here; this also means that using any Pythontempfile
default behavior works),meta.yaml
contains a link to the documentation of the respective tool or command,Snakefile
s pass the linting (snakemake --lint
),Snakefile
s are formatted with snakefmt,